Starting phenix.real_space_refine on Thu Jul 31 18:13:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kln_62410/07_2025/9kln_62410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kln_62410/07_2025/9kln_62410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2025/9kln_62410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2025/9kln_62410.map" model { file = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2025/9kln_62410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kln_62410/07_2025/9kln_62410.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 143 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 8118 2.51 5 N 2535 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13749 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1385, 10685 Classifications: {'peptide': 1385} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 57, 'TRANS': 1327} Chain breaks: 13 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'GLU:plan': 19, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 177 Chain: "B" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2204 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 40} Link IDs: {'rna2p': 15, 'rna3p': 87} Chain breaks: 1 Chain: "C" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 8} Link IDs: {None: 9} Time building chain proxies: 8.86, per 1000 atoms: 0.64 Number of scatterers: 13749 At special positions: 0 Unit cell: (104.648, 119.48, 126.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 143 15.00 Mg 2 11.99 O 2915 8.00 N 2535 7.00 C 8118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2586 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 55.4% alpha, 9.0% beta 50 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 52 Processing helix chain 'A' and resid 53 through 54 No H-bonds generated for 'chain 'A' and resid 53 through 54' Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 106 through 125 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 175 through 185 removed outlier: 4.096A pdb=" N MET A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 234 through 252 Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 278 through 287 removed outlier: 3.725A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.548A pdb=" N GLY A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.690A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.662A pdb=" N THR A 369 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 416 Processing helix chain 'A' and resid 417 through 418 No H-bonds generated for 'chain 'A' and resid 417 through 418' Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.835A pdb=" N ALA A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.634A pdb=" N ILE A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.566A pdb=" N GLU A 664 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.662A pdb=" N LYS A 746 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.505A pdb=" N TRP A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 936 through 966 removed outlier: 4.144A pdb=" N LYS A 953 " --> pdb=" O ARG A 949 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 998 through 1015 removed outlier: 3.584A pdb=" N ASP A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1029 Processing helix chain 'A' and resid 1054 through 1073 Proline residue: A1066 - end of helix Processing helix chain 'A' and resid 1075 through 1108 removed outlier: 3.602A pdb=" N LYS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1115 Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.996A pdb=" N ILE A1119 " --> pdb=" O THR A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1139 Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'A' and resid 1162 through 1190 Processing helix chain 'A' and resid 1234 through 1243 Processing helix chain 'A' and resid 1244 through 1258 Processing helix chain 'A' and resid 1269 through 1273 removed outlier: 3.818A pdb=" N GLN A1273 " --> pdb=" O THR A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1309 Processing helix chain 'A' and resid 1311 through 1323 removed outlier: 3.575A pdb=" N ARG A1315 " --> pdb=" O THR A1311 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A1323 " --> pdb=" O ALA A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 3.933A pdb=" N GLY A1336 " --> pdb=" O GLU A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.628A pdb=" N LYS A1359 " --> pdb=" O PRO A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1377 Processing helix chain 'A' and resid 1457 through 1481 removed outlier: 3.640A pdb=" N ASN A1481 " --> pdb=" O LEU A1477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.750A pdb=" N ALA A 101 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASN A 155 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 99 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.331A pdb=" N LEU A 356 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 637 removed outlier: 6.167A pdb=" N ALA A 635 " --> pdb=" O THR A 657 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 812 removed outlier: 3.676A pdb=" N ARG A 810 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 21.329A pdb=" N GLU A 824 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 16.706A pdb=" N PHE A 854 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 13.223A pdb=" N SER A 826 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ARG A 852 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL A 828 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 778 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN A 853 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS A 776 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 855 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 774 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A1220 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A1217 " --> pdb=" O ARG A1263 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A1265 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A1219 " --> pdb=" O VAL A1265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 969 through 972 Processing sheet with id=AA7, first strand: chain 'A' and resid 1338 through 1341 Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1390 586 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3027 1.33 - 1.45: 3875 1.45 - 1.57: 7074 1.57 - 1.70: 284 1.70 - 1.82: 57 Bond restraints: 14317 Sorted by residual: bond pdb=" CA GLY A 228 " pdb=" C GLY A 228 " ideal model delta sigma weight residual 1.517 1.569 -0.052 9.60e-03 1.09e+04 2.92e+01 bond pdb=" C GLY A 228 " pdb=" N THR A 229 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.36e-02 5.41e+03 2.52e+01 bond pdb=" N ILE A 497 " pdb=" CA ILE A 497 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.98e+00 bond pdb=" N ILE A 167 " pdb=" CA ILE A 167 " ideal model delta sigma weight residual 1.462 1.494 -0.031 1.14e-02 7.69e+03 7.62e+00 bond pdb=" N VAL A1194 " pdb=" CA VAL A1194 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.25e-02 6.40e+03 7.00e+00 ... (remaining 14312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 19017 1.70 - 3.39: 740 3.39 - 5.09: 169 5.09 - 6.79: 98 6.79 - 8.48: 14 Bond angle restraints: 20038 Sorted by residual: angle pdb=" O3' A B 20 " pdb=" P G B 21 " pdb=" O5' G B 21 " ideal model delta sigma weight residual 104.00 95.59 8.41 1.50e+00 4.44e-01 3.14e+01 angle pdb=" C4' G B 27 " pdb=" C3' G B 27 " pdb=" C2' G B 27 " ideal model delta sigma weight residual 102.60 98.08 4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" O3' G B 49 " pdb=" P G B 50 " pdb=" O5' G B 50 " ideal model delta sigma weight residual 104.00 97.67 6.33 1.50e+00 4.44e-01 1.78e+01 angle pdb=" C4' G B 92 " pdb=" C3' G B 92 " pdb=" O3' G B 92 " ideal model delta sigma weight residual 109.40 115.66 -6.26 1.50e+00 4.44e-01 1.74e+01 angle pdb=" C4' C B 107 " pdb=" C3' C B 107 " pdb=" C2' C B 107 " ideal model delta sigma weight residual 102.60 98.52 4.08 1.00e+00 1.00e+00 1.66e+01 ... (remaining 20033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 7913 34.73 - 69.45: 657 69.45 - 104.18: 54 104.18 - 138.90: 0 138.90 - 173.63: 1 Dihedral angle restraints: 8625 sinusoidal: 4637 harmonic: 3988 Sorted by residual: dihedral pdb=" CD ARG A 166 " pdb=" NE ARG A 166 " pdb=" CZ ARG A 166 " pdb=" NH1 ARG A 166 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" O4' C B 45 " pdb=" C1' C B 45 " pdb=" N1 C B 45 " pdb=" C2 C B 45 " ideal model delta sinusoidal sigma weight residual 200.00 26.37 173.63 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" CD ARG A1196 " pdb=" NE ARG A1196 " pdb=" CZ ARG A1196 " pdb=" NH1 ARG A1196 " ideal model delta sinusoidal sigma weight residual 0.00 60.90 -60.90 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 8622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2118 0.115 - 0.230: 97 0.230 - 0.345: 17 0.345 - 0.459: 34 0.459 - 0.574: 14 Chirality restraints: 2280 Sorted by residual: chirality pdb=" P C B 82 " pdb=" OP1 C B 82 " pdb=" OP2 C B 82 " pdb=" O5' C B 82 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" P DC D 5 " pdb=" OP1 DC D 5 " pdb=" OP2 DC D 5 " pdb=" O5' DC D 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" P DA C 31 " pdb=" OP1 DA C 31 " pdb=" OP2 DA C 31 " pdb=" O5' DA C 31 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.12e+00 ... (remaining 2277 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 166 " 1.096 9.50e-02 1.11e+02 4.91e-01 1.46e+02 pdb=" NE ARG A 166 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 166 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 166 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 166 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1196 " 0.958 9.50e-02 1.11e+02 4.29e-01 1.12e+02 pdb=" NE ARG A1196 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A1196 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A1196 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1196 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1193 " -0.638 9.50e-02 1.11e+02 2.86e-01 4.99e+01 pdb=" NE ARG A1193 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A1193 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A1193 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1193 " -0.020 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 150 2.61 - 3.19: 11382 3.19 - 3.76: 23462 3.76 - 4.33: 31963 4.33 - 4.90: 49582 Nonbonded interactions: 116539 Sorted by model distance: nonbonded pdb="MG MG B 202 " pdb=" O HOH B 302 " model vdw 2.042 2.170 nonbonded pdb=" OP2 C B 39 " pdb="MG MG B 202 " model vdw 2.048 2.170 nonbonded pdb="MG MG B 201 " pdb=" O HOH B 308 " model vdw 2.069 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 304 " model vdw 2.086 2.170 nonbonded pdb=" OP2 U B 33 " pdb="MG MG B 201 " model vdw 2.098 2.170 ... (remaining 116534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 40.070 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14317 Z= 0.357 Angle : 0.875 8.482 20038 Z= 0.481 Chirality : 0.084 0.574 2280 Planarity : 0.016 0.491 2055 Dihedral : 21.238 173.626 6039 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 2.00 % Allowed : 21.93 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1357 helix: 1.53 (0.20), residues: 701 sheet: -0.45 (0.45), residues: 126 loop : -0.64 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 30 HIS 0.005 0.001 HIS A 392 PHE 0.013 0.002 PHE A 386 TYR 0.016 0.002 TYR A 954 ARG 0.016 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.16209 ( 715) hydrogen bonds : angle 6.64484 ( 1909) covalent geometry : bond 0.00693 (14317) covalent geometry : angle 0.87546 (20038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8445 (m-30) cc_final: 0.7958 (m-30) REVERT: A 326 LYS cc_start: 0.5713 (tttt) cc_final: 0.5408 (mtmt) REVERT: A 375 ASP cc_start: 0.8291 (p0) cc_final: 0.7564 (t0) REVERT: A 413 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6664 (mtt90) REVERT: A 439 ARG cc_start: 0.6255 (mmm160) cc_final: 0.5628 (mpp-170) REVERT: A 485 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.5184 (mt) REVERT: A 539 LYS cc_start: 0.7427 (mtpp) cc_final: 0.6961 (mttp) REVERT: A 652 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7680 (tpm170) REVERT: A 696 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8119 (mt-10) REVERT: A 780 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: A 878 MET cc_start: 0.8395 (ttm) cc_final: 0.8120 (ttp) REVERT: A 916 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8571 (mttp) REVERT: A 941 MET cc_start: 0.9101 (mmm) cc_final: 0.8690 (mmp) REVERT: A 1158 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8691 (mtmt) REVERT: A 1245 SER cc_start: 0.8196 (t) cc_final: 0.7962 (p) REVERT: A 1247 VAL cc_start: 0.9360 (t) cc_final: 0.9064 (p) REVERT: A 1248 LYS cc_start: 0.8596 (tttt) cc_final: 0.8266 (tppt) REVERT: A 1294 ASN cc_start: 0.6451 (OUTLIER) cc_final: 0.6058 (m110) REVERT: A 1329 MET cc_start: 0.3283 (mmp) cc_final: 0.2790 (mtp) REVERT: A 1352 ASP cc_start: 0.8038 (t70) cc_final: 0.7589 (t0) REVERT: A 1464 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8084 (tm-30) outliers start: 21 outliers final: 2 residues processed: 192 average time/residue: 1.7461 time to fit residues: 359.4072 Evaluate side-chains 102 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1294 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 45 optimal weight: 0.0050 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 137 optimal weight: 0.1980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096433 restraints weight = 19817.471| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.08 r_work: 0.3120 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14317 Z= 0.126 Angle : 0.539 11.133 20038 Z= 0.285 Chirality : 0.035 0.336 2280 Planarity : 0.004 0.043 2055 Dihedral : 19.933 179.633 3572 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.19 % Allowed : 22.59 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1357 helix: 1.98 (0.20), residues: 708 sheet: -0.17 (0.46), residues: 125 loop : -0.51 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 30 HIS 0.004 0.001 HIS A 56 PHE 0.009 0.001 PHE A 562 TYR 0.019 0.001 TYR A1458 ARG 0.007 0.000 ARG A1020 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 715) hydrogen bonds : angle 3.94077 ( 1909) covalent geometry : bond 0.00256 (14317) covalent geometry : angle 0.53920 (20038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7265 (ttm170) REVERT: A 326 LYS cc_start: 0.6554 (tttt) cc_final: 0.6010 (mtmt) REVERT: A 375 ASP cc_start: 0.8353 (p0) cc_final: 0.7394 (t0) REVERT: A 413 ARG cc_start: 0.6900 (ttm170) cc_final: 0.6527 (mtt90) REVERT: A 431 TRP cc_start: 0.6908 (t60) cc_final: 0.6451 (t-100) REVERT: A 439 ARG cc_start: 0.6464 (mmm160) cc_final: 0.5754 (mpp-170) REVERT: A 453 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7446 (mmt-90) REVERT: A 485 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5207 (mt) REVERT: A 539 LYS cc_start: 0.7088 (mtpp) cc_final: 0.6632 (mttp) REVERT: A 652 ARG cc_start: 0.8052 (ttt-90) cc_final: 0.7559 (tpm170) REVERT: A 696 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7983 (mt-10) REVERT: A 732 GLN cc_start: 0.6720 (mp10) cc_final: 0.6274 (mm110) REVERT: A 878 MET cc_start: 0.8220 (ttm) cc_final: 0.7898 (ttp) REVERT: A 939 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: A 1158 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8578 (mtmt) REVERT: A 1245 SER cc_start: 0.7949 (t) cc_final: 0.7562 (p) REVERT: A 1247 VAL cc_start: 0.9196 (t) cc_final: 0.8897 (p) REVERT: A 1248 LYS cc_start: 0.8677 (tttt) cc_final: 0.8183 (tppt) REVERT: A 1329 MET cc_start: 0.2965 (mmp) cc_final: 0.2746 (mtt) REVERT: A 1335 MET cc_start: 0.4599 (mmm) cc_final: 0.4312 (mmm) REVERT: A 1352 ASP cc_start: 0.7862 (t70) cc_final: 0.7363 (t0) REVERT: A 1359 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7762 (mtpt) REVERT: A 1400 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5849 (tm-30) REVERT: A 1464 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7942 (tm-30) outliers start: 44 outliers final: 15 residues processed: 149 average time/residue: 1.4160 time to fit residues: 229.7001 Evaluate side-chains 114 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 897 TRP Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1478 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN A 813 GLN A1301 GLN A1471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092093 restraints weight = 19710.644| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.91 r_work: 0.3045 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14317 Z= 0.202 Angle : 0.565 12.955 20038 Z= 0.299 Chirality : 0.038 0.419 2280 Planarity : 0.004 0.046 2055 Dihedral : 19.692 173.210 3565 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.72 % Allowed : 23.36 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1357 helix: 1.96 (0.19), residues: 701 sheet: -0.30 (0.46), residues: 124 loop : -0.54 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 30 HIS 0.004 0.001 HIS A 556 PHE 0.014 0.001 PHE A 386 TYR 0.016 0.002 TYR A 954 ARG 0.006 0.001 ARG A1462 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 715) hydrogen bonds : angle 3.90865 ( 1909) covalent geometry : bond 0.00438 (14317) covalent geometry : angle 0.56516 (20038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7401 (ttm170) REVERT: A 326 LYS cc_start: 0.6692 (tttt) cc_final: 0.6087 (mtmt) REVERT: A 330 SER cc_start: 0.7511 (m) cc_final: 0.7294 (p) REVERT: A 413 ARG cc_start: 0.6977 (ttm170) cc_final: 0.6559 (mtt90) REVERT: A 485 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5436 (mt) REVERT: A 541 ARG cc_start: 0.8480 (ptp-110) cc_final: 0.8015 (ptt90) REVERT: A 624 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 652 ARG cc_start: 0.8015 (ttt-90) cc_final: 0.7585 (tpm170) REVERT: A 696 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8293 (mm-30) REVERT: A 813 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: A 982 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: A 1158 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8599 (mtmt) REVERT: A 1245 SER cc_start: 0.7979 (t) cc_final: 0.7565 (p) REVERT: A 1247 VAL cc_start: 0.9178 (t) cc_final: 0.8955 (p) REVERT: A 1309 LYS cc_start: 0.8167 (tppt) cc_final: 0.7646 (tptp) REVERT: A 1335 MET cc_start: 0.5001 (mmm) cc_final: 0.4693 (mmm) REVERT: A 1352 ASP cc_start: 0.7862 (t70) cc_final: 0.7300 (t0) REVERT: A 1359 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7866 (mtpt) REVERT: A 1400 GLU cc_start: 0.6285 (mm-30) cc_final: 0.6063 (tm-30) REVERT: A 1478 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7375 (ptpp) outliers start: 39 outliers final: 12 residues processed: 137 average time/residue: 1.4200 time to fit residues: 211.5522 Evaluate side-chains 110 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 813 GLN Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1359 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1478 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN A 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094645 restraints weight = 19704.028| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.04 r_work: 0.3087 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14317 Z= 0.116 Angle : 0.495 13.219 20038 Z= 0.264 Chirality : 0.034 0.388 2280 Planarity : 0.004 0.042 2055 Dihedral : 19.474 178.572 3565 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.00 % Allowed : 23.36 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1357 helix: 2.22 (0.19), residues: 704 sheet: -0.29 (0.46), residues: 124 loop : -0.45 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 30 HIS 0.002 0.001 HIS A 876 PHE 0.012 0.001 PHE A 435 TYR 0.018 0.001 TYR A1458 ARG 0.008 0.000 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 715) hydrogen bonds : angle 3.59089 ( 1909) covalent geometry : bond 0.00239 (14317) covalent geometry : angle 0.49519 (20038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7284 (ttm170) REVERT: A 284 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6429 (mmtm) REVERT: A 326 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6010 (mtmt) REVERT: A 413 ARG cc_start: 0.6885 (ttm170) cc_final: 0.6468 (mtt90) REVERT: A 485 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5505 (mt) REVERT: A 541 ARG cc_start: 0.8491 (ptp-110) cc_final: 0.7982 (ptt90) REVERT: A 652 ARG cc_start: 0.7987 (ttt-90) cc_final: 0.7578 (tpm170) REVERT: A 696 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8260 (mm-30) REVERT: A 717 ARG cc_start: 0.8672 (mmt-90) cc_final: 0.8428 (mpt180) REVERT: A 825 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: A 878 MET cc_start: 0.8244 (ttm) cc_final: 0.7864 (ttp) REVERT: A 1000 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8065 (ptpp) REVERT: A 1158 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8560 (mtmt) REVERT: A 1245 SER cc_start: 0.7873 (t) cc_final: 0.7418 (p) REVERT: A 1247 VAL cc_start: 0.9135 (t) cc_final: 0.8902 (p) REVERT: A 1309 LYS cc_start: 0.8107 (tppt) cc_final: 0.7501 (tptp) REVERT: A 1335 MET cc_start: 0.4984 (mmm) cc_final: 0.4723 (mmm) REVERT: A 1352 ASP cc_start: 0.7753 (t70) cc_final: 0.7212 (t0) REVERT: A 1400 GLU cc_start: 0.6286 (mm-30) cc_final: 0.6066 (tm-30) REVERT: A 1464 GLU cc_start: 0.8352 (tp30) cc_final: 0.7670 (tm-30) outliers start: 42 outliers final: 17 residues processed: 132 average time/residue: 1.4211 time to fit residues: 203.8230 Evaluate side-chains 112 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 105 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090333 restraints weight = 19713.978| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.95 r_work: 0.3015 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14317 Z= 0.246 Angle : 0.580 14.062 20038 Z= 0.305 Chirality : 0.039 0.432 2280 Planarity : 0.005 0.059 2055 Dihedral : 19.590 173.535 3562 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.19 % Allowed : 22.69 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1357 helix: 2.07 (0.19), residues: 702 sheet: -0.40 (0.46), residues: 125 loop : -0.54 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1102 HIS 0.004 0.001 HIS A 317 PHE 0.016 0.002 PHE A 386 TYR 0.015 0.002 TYR A1387 ARG 0.010 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 715) hydrogen bonds : angle 3.83603 ( 1909) covalent geometry : bond 0.00536 (14317) covalent geometry : angle 0.57974 (20038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7329 (ttm170) REVERT: A 326 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6082 (mtmt) REVERT: A 413 ARG cc_start: 0.6961 (ttm170) cc_final: 0.6522 (mtt90) REVERT: A 485 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5426 (mt) REVERT: A 541 ARG cc_start: 0.8524 (ptp-110) cc_final: 0.7997 (ptt90) REVERT: A 624 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7790 (mp) REVERT: A 652 ARG cc_start: 0.8030 (ttt-90) cc_final: 0.7561 (tpm170) REVERT: A 736 LYS cc_start: 0.8225 (pttt) cc_final: 0.7634 (ptpt) REVERT: A 825 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: A 939 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: A 1000 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8123 (ptpp) REVERT: A 1158 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8567 (mtmt) REVERT: A 1245 SER cc_start: 0.7988 (t) cc_final: 0.7556 (p) REVERT: A 1247 VAL cc_start: 0.9126 (t) cc_final: 0.8878 (p) REVERT: A 1309 LYS cc_start: 0.8072 (tppt) cc_final: 0.7296 (tptt) REVERT: A 1335 MET cc_start: 0.5072 (mmm) cc_final: 0.4798 (mmm) REVERT: A 1352 ASP cc_start: 0.7750 (t70) cc_final: 0.7130 (t0) REVERT: A 1400 GLU cc_start: 0.6349 (mm-30) cc_final: 0.6112 (tm-30) REVERT: A 1449 PRO cc_start: 0.7928 (Cg_exo) cc_final: 0.7713 (Cg_endo) outliers start: 44 outliers final: 19 residues processed: 127 average time/residue: 1.5015 time to fit residues: 206.8288 Evaluate side-chains 112 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1477 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088496 restraints weight = 19830.221| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.95 r_work: 0.2985 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 14317 Z= 0.388 Angle : 0.691 14.426 20038 Z= 0.362 Chirality : 0.046 0.463 2280 Planarity : 0.006 0.057 2055 Dihedral : 19.897 175.228 3562 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.34 % Allowed : 21.64 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1357 helix: 1.52 (0.19), residues: 709 sheet: -0.50 (0.46), residues: 123 loop : -0.77 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1102 HIS 0.006 0.001 HIS A 317 PHE 0.020 0.002 PHE A 386 TYR 0.018 0.003 TYR A1458 ARG 0.006 0.001 ARG A1129 Details of bonding type rmsd hydrogen bonds : bond 0.05756 ( 715) hydrogen bonds : angle 4.19493 ( 1909) covalent geometry : bond 0.00852 (14317) covalent geometry : angle 0.69125 (20038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 90 time to evaluate : 1.318 Fit side-chains REVERT: A 73 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7394 (mp) REVERT: A 273 SER cc_start: 0.8106 (t) cc_final: 0.7770 (m) REVERT: A 322 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6707 (mt-10) REVERT: A 326 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6154 (mtmt) REVERT: A 413 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6576 (mtt90) REVERT: A 439 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6216 (mtt180) REVERT: A 453 ARG cc_start: 0.8267 (mmt180) cc_final: 0.7999 (mmt90) REVERT: A 454 ARG cc_start: 0.7573 (ttt180) cc_final: 0.7133 (tpt90) REVERT: A 485 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5270 (mt) REVERT: A 505 GLN cc_start: 0.6754 (mm110) cc_final: 0.6392 (mp10) REVERT: A 541 ARG cc_start: 0.8529 (ptp-110) cc_final: 0.8026 (ptt90) REVERT: A 624 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.7884 (mp) REVERT: A 652 ARG cc_start: 0.8153 (ttt-90) cc_final: 0.7621 (tpm170) REVERT: A 736 LYS cc_start: 0.8320 (pttt) cc_final: 0.7879 (pttm) REVERT: A 939 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: A 1158 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8685 (mtmt) REVERT: A 1245 SER cc_start: 0.8006 (t) cc_final: 0.7665 (p) REVERT: A 1248 LYS cc_start: 0.8780 (tttt) cc_final: 0.8500 (tmtt) REVERT: A 1309 LYS cc_start: 0.8230 (tppt) cc_final: 0.7460 (tptt) REVERT: A 1352 ASP cc_start: 0.7832 (t70) cc_final: 0.7136 (t0) outliers start: 56 outliers final: 20 residues processed: 137 average time/residue: 1.5075 time to fit residues: 223.6793 Evaluate side-chains 110 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 813 GLN A1294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093239 restraints weight = 19636.607| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.88 r_work: 0.3065 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14317 Z= 0.146 Angle : 0.534 15.278 20038 Z= 0.283 Chirality : 0.036 0.392 2280 Planarity : 0.004 0.035 2055 Dihedral : 19.536 178.639 3562 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.81 % Allowed : 23.26 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1357 helix: 2.12 (0.19), residues: 701 sheet: -0.33 (0.46), residues: 125 loop : -0.55 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1102 HIS 0.003 0.001 HIS A 556 PHE 0.018 0.001 PHE A 435 TYR 0.016 0.001 TYR A1387 ARG 0.007 0.000 ARG A1462 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 715) hydrogen bonds : angle 3.73052 ( 1909) covalent geometry : bond 0.00308 (14317) covalent geometry : angle 0.53423 (20038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.200 Fit side-chains REVERT: A 41 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7486 (ttm170) REVERT: A 326 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6095 (mtmt) REVERT: A 413 ARG cc_start: 0.7024 (ttm170) cc_final: 0.6575 (mtt90) REVERT: A 453 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7940 (mmt90) REVERT: A 454 ARG cc_start: 0.7602 (ttt180) cc_final: 0.7033 (tpt170) REVERT: A 485 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5369 (mp) REVERT: A 541 ARG cc_start: 0.8510 (ptp-110) cc_final: 0.7998 (ptt90) REVERT: A 652 ARG cc_start: 0.8097 (ttt-90) cc_final: 0.7606 (tpm170) REVERT: A 717 ARG cc_start: 0.8699 (mmt-90) cc_final: 0.8386 (mpt180) REVERT: A 736 LYS cc_start: 0.8263 (pttt) cc_final: 0.7772 (pttm) REVERT: A 878 MET cc_start: 0.8436 (ttm) cc_final: 0.8028 (ttp) REVERT: A 939 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: A 1017 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8149 (mmt180) REVERT: A 1158 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8641 (mtmt) REVERT: A 1245 SER cc_start: 0.7925 (t) cc_final: 0.7496 (p) REVERT: A 1247 VAL cc_start: 0.9176 (t) cc_final: 0.8943 (p) REVERT: A 1248 LYS cc_start: 0.8807 (tttt) cc_final: 0.8498 (tmtt) REVERT: A 1309 LYS cc_start: 0.8217 (tppt) cc_final: 0.7337 (tptt) REVERT: A 1352 ASP cc_start: 0.7885 (t70) cc_final: 0.7276 (t0) outliers start: 40 outliers final: 17 residues processed: 123 average time/residue: 1.5098 time to fit residues: 201.2456 Evaluate side-chains 109 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1017 ARG Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.090347 restraints weight = 19645.752| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.90 r_work: 0.3018 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14317 Z= 0.257 Angle : 0.594 16.030 20038 Z= 0.312 Chirality : 0.040 0.427 2280 Planarity : 0.005 0.036 2055 Dihedral : 19.591 175.055 3562 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.24 % Allowed : 24.02 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1357 helix: 2.00 (0.19), residues: 702 sheet: -0.31 (0.46), residues: 123 loop : -0.58 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 431 HIS 0.004 0.001 HIS A 392 PHE 0.018 0.001 PHE A 435 TYR 0.018 0.002 TYR A1387 ARG 0.007 0.001 ARG A1462 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 715) hydrogen bonds : angle 3.88642 ( 1909) covalent geometry : bond 0.00560 (14317) covalent geometry : angle 0.59439 (20038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 1.300 Fit side-chains REVERT: A 41 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7485 (ttm170) REVERT: A 86 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 326 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6094 (mtmt) REVERT: A 328 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7320 (mtpt) REVERT: A 413 ARG cc_start: 0.6992 (ttm170) cc_final: 0.6576 (mtt90) REVERT: A 439 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6217 (mtt180) REVERT: A 453 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7961 (mmt90) REVERT: A 454 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7100 (tpt170) REVERT: A 485 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5460 (mp) REVERT: A 541 ARG cc_start: 0.8521 (ptp-110) cc_final: 0.7981 (ptt90) REVERT: A 652 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7591 (tpm170) REVERT: A 736 LYS cc_start: 0.8284 (pttt) cc_final: 0.7843 (pttm) REVERT: A 939 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: A 1158 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8658 (mtmt) REVERT: A 1245 SER cc_start: 0.7997 (t) cc_final: 0.7564 (p) REVERT: A 1247 VAL cc_start: 0.9190 (t) cc_final: 0.8949 (p) REVERT: A 1248 LYS cc_start: 0.8812 (tttt) cc_final: 0.8505 (tmtt) REVERT: A 1309 LYS cc_start: 0.8188 (tppt) cc_final: 0.7309 (tptt) REVERT: A 1352 ASP cc_start: 0.7865 (t70) cc_final: 0.7242 (t0) outliers start: 34 outliers final: 21 residues processed: 114 average time/residue: 1.5637 time to fit residues: 192.6459 Evaluate side-chains 110 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1017 ARG Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 112 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089529 restraints weight = 19478.005| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.88 r_work: 0.3004 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14317 Z= 0.289 Angle : 0.630 16.153 20038 Z= 0.330 Chirality : 0.041 0.439 2280 Planarity : 0.005 0.039 2055 Dihedral : 19.668 174.657 3562 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.62 % Allowed : 23.55 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1357 helix: 1.78 (0.19), residues: 709 sheet: -0.35 (0.46), residues: 123 loop : -0.67 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 431 HIS 0.005 0.001 HIS A 392 PHE 0.018 0.002 PHE A 435 TYR 0.020 0.002 TYR A1387 ARG 0.007 0.001 ARG A1462 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 715) hydrogen bonds : angle 3.99419 ( 1909) covalent geometry : bond 0.00632 (14317) covalent geometry : angle 0.62985 (20038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 1.286 Fit side-chains REVERT: A 41 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7477 (ttm170) REVERT: A 58 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 86 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8734 (mm) REVERT: A 326 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6092 (mtmt) REVERT: A 328 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7344 (mtpt) REVERT: A 413 ARG cc_start: 0.6962 (ttm170) cc_final: 0.6545 (mtt90) REVERT: A 439 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6262 (mtt180) REVERT: A 453 ARG cc_start: 0.8335 (mmt180) cc_final: 0.8034 (mmt90) REVERT: A 541 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8060 (ptt90) REVERT: A 652 ARG cc_start: 0.8123 (ttt-90) cc_final: 0.7618 (tpm170) REVERT: A 736 LYS cc_start: 0.8302 (pttt) cc_final: 0.7853 (pttm) REVERT: A 916 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8643 (mmmt) REVERT: A 939 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8219 (mm-30) REVERT: A 1000 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8255 (ptpp) REVERT: A 1158 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8676 (mtmt) REVERT: A 1245 SER cc_start: 0.7997 (t) cc_final: 0.7560 (p) REVERT: A 1248 LYS cc_start: 0.8812 (tttt) cc_final: 0.8529 (tmtt) REVERT: A 1309 LYS cc_start: 0.8207 (tppt) cc_final: 0.7289 (tptt) REVERT: A 1352 ASP cc_start: 0.7864 (t70) cc_final: 0.7225 (t0) outliers start: 38 outliers final: 22 residues processed: 110 average time/residue: 1.7230 time to fit residues: 204.5158 Evaluate side-chains 108 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1017 ARG Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 134 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 688 GLN A 813 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.135305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094282 restraints weight = 19639.060| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.88 r_work: 0.3082 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14317 Z= 0.132 Angle : 0.521 15.826 20038 Z= 0.277 Chirality : 0.035 0.387 2280 Planarity : 0.004 0.038 2055 Dihedral : 19.385 178.790 3560 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.38 % Allowed : 24.69 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1357 helix: 2.14 (0.19), residues: 713 sheet: -0.30 (0.46), residues: 125 loop : -0.49 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 431 HIS 0.002 0.001 HIS A 556 PHE 0.018 0.001 PHE A 435 TYR 0.016 0.001 TYR A1387 ARG 0.008 0.000 ARG A1462 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 715) hydrogen bonds : angle 3.66600 ( 1909) covalent geometry : bond 0.00279 (14317) covalent geometry : angle 0.52068 (20038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.266 Fit side-chains REVERT: A 41 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7442 (ttm170) REVERT: A 326 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6289 (ptpt) REVERT: A 328 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7310 (mtpt) REVERT: A 413 ARG cc_start: 0.6922 (ttm170) cc_final: 0.6500 (mtt90) REVERT: A 453 ARG cc_start: 0.8318 (mmt180) cc_final: 0.8031 (mmt90) REVERT: A 454 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7104 (tpt170) REVERT: A 541 ARG cc_start: 0.8496 (ptp-110) cc_final: 0.7927 (ptt90) REVERT: A 652 ARG cc_start: 0.8069 (ttt-90) cc_final: 0.7603 (tpm170) REVERT: A 717 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8371 (mpt180) REVERT: A 736 LYS cc_start: 0.8203 (pttt) cc_final: 0.7678 (pttm) REVERT: A 878 MET cc_start: 0.8410 (ttm) cc_final: 0.8012 (ttp) REVERT: A 939 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: A 1158 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8591 (mtmt) REVERT: A 1245 SER cc_start: 0.7927 (t) cc_final: 0.7489 (p) REVERT: A 1247 VAL cc_start: 0.9165 (t) cc_final: 0.8947 (p) REVERT: A 1248 LYS cc_start: 0.8814 (tttt) cc_final: 0.8501 (tmtt) REVERT: A 1309 LYS cc_start: 0.8215 (tppt) cc_final: 0.7320 (tptt) REVERT: A 1352 ASP cc_start: 0.7891 (t70) cc_final: 0.7599 (t0) outliers start: 25 outliers final: 16 residues processed: 105 average time/residue: 1.6031 time to fit residues: 181.8177 Evaluate side-chains 102 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 939 GLU Chi-restraints excluded: chain A residue 1017 ARG Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 126 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 0.0170 chunk 18 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 129 optimal weight: 0.0010 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095412 restraints weight = 19747.524| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.88 r_work: 0.3100 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 14317 Z= 0.109 Angle : 0.520 16.131 20038 Z= 0.275 Chirality : 0.035 0.382 2280 Planarity : 0.004 0.061 2055 Dihedral : 19.382 177.306 3560 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 25.36 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1357 helix: 2.24 (0.19), residues: 716 sheet: -0.26 (0.47), residues: 125 loop : -0.39 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 431 HIS 0.002 0.001 HIS A 556 PHE 0.017 0.001 PHE A 435 TYR 0.020 0.001 TYR A1387 ARG 0.009 0.000 ARG A1462 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 715) hydrogen bonds : angle 3.60745 ( 1909) covalent geometry : bond 0.00225 (14317) covalent geometry : angle 0.52003 (20038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11379.69 seconds wall clock time: 193 minutes 46.87 seconds (11626.87 seconds total)